commit af0fe23c4f7abb07b1e74df46596171cd53e814b
Date:   Tue Sep 26 16:49:01 2017 -0400

    RosettaAI: Setting rosetta_scripts_scripts submodule to latest origin/master version.

commit d6b45ae5514df4f6f109085a4ccc6dc770243381
Date:   Tue Sep 26 10:27:02 2017 -0500

    Beautifying forgotten file.

commit 75460266bdf98bbd346c114c7e07653c487a1d80
Merge: e48877f 8d24299
Date:   Tue Sep 26 09:56:38 2017 -0500

    Merge pull request #2556 from RosettaCommons/roccomoretti/xml_to_MMfactory
    
    Change parse_my_tag() to use MoveMapFactories.
    
    The parse_movemap() functionality used in parse_my_tag() took a Pose. This was less than desirable, as there's no guarantee that the pose that the move map will be used on will be related in any significant way to the input pose being passed to parse_my_tag().
    
    Now the parse_my_tag() will generate a core::select::movemap::MoveMapFactory object from the tag specification, rather than a MoveMap itself. This will be then applied against the pose in the apply() function to get a MoveMap that is actually used. By waiting for apply() (and re-generating the MoveMap for each call to apply), the MoveMap thus generated will reflect the status of the pose as it is then, rather than the pose as it was in the input.

commit e48877f42cfc459b9aa549c6c2a8638c819934f7
Date:   Mon Sep 25 19:54:39 2017 -0700

    Reducing the sigfigs for the cenrot unit test comparisons because compilers and reasons and that's too much precision anyway

commit 9f16acbccaae537eb3d2efba51432be09a38d80e
Date:   Mon Sep 25 18:07:34 2017 -0700

    Modifying etable unit tests to fix a linking error with clang 9.0

commit b44020c5aab410a57169c431ba12a4ba4eec8496
Date:   Mon Sep 25 15:30:58 2017 -0700

    Updating setup_platforms.py for macOS High Sierra

commit c24e46cdc406faef7d6555cf5224255e9c47f385
Date:   Mon Sep 25 15:30:36 2017 -0700

    Updating setup_platforms.py for macOS High Sierra

commit 3e5835f2c95cb9b91ac5c4519576e4b21e5acd7e
Merge: d0dd849 3ad0e7d
Date:   Mon Sep 25 14:54:56 2017 -0700

    Merge pull request #2554 from RosettaCommons/everyday847/repair_new_align_pdb
    
    Repair assignment of align_pose vs. native pose

commit d0dd8491da3f250d77dee63cb52efce950586896
Merge: 9e757a2 cf8b39a
Date:   Mon Sep 25 12:28:34 2017 -0700

    Merge pull request #2572 from RosettaCommons/basantab/fix_ConsensusLoopDes_doubleHis
    
    Bug fix for ConsensusLoopDesign: His was added twice

commit 9e757a28e8213df6d0c36dc4aeb9d659a19b42bc
Merge: a8dfc3f 0c83759
Date:   Mon Sep 25 11:50:45 2017 -0400

    Merge pull request #2577 from RosettaCommons/JackMaguire/monte_carlo_hbnet
    
    Small bug fixes in Monte Carlo HBNet

commit a8dfc3f6d83e12c581fea4f529140b245d784322
Merge: 711915a 8000520
Date:   Mon Sep 25 08:08:45 2017 -0700

    merge with master

commit 711915a3ca9b0dd01820f3f8825678b81df5aeef
Merge: 16fcd33 b943dce
Date:   Mon Sep 25 08:08:23 2017 -0700

    merge again with master

commit 16fcd331a1c46ece5d4fabc88a66e761761562b1
Merge: 6445198 be47202
Date:   Sun Sep 24 21:16:02 2017 -0400

    Merge pull request #2560 from RosettaCommons/smlewis/cyrus/XMLs_from_XRW_rosettascriptstestbranch
    
    Update rosetta_scripts_scripts submodule with cyrus-sourced XSD XRW scripts.  Also update with a bunch of other people's scripts, apparently.  I'm tired of the "wait for test server results, oh, someone has changed the base version, you have to test again" dance.

commit 644519856ca23111b5aa0945ee3ca0d33c39989f
Merge: 97d00e0 0c440e8
Date:   Fri Sep 22 21:22:45 2017 -0400

    Adding mangling of developer email info in git output so it raw email does not appear in test log

commit 97d00e0e2acb6df20d5673eabb893777692dd9b0
Date:   Fri Sep 22 20:56:37 2017 -0400

    RosettaAI: Setting pyrosetta_scripts submodule to latest origin/master version.

commit 0d5f0dd292bf75e6ef40131a8b57927bf9b02605
Date:   Fri Sep 22 16:55:08 2017 -0400

    RosettaAI: Setting pyrosetta_scripts submodule to latest origin/master version.

commit d3ebe63392e6c967817dfff6198bd29d485c1f7c
Merge: 574c504 28cacf0
Date:   Fri Sep 22 14:31:00 2017 -0600

    Merge pull request #2558 from RosettaCommons/benchmark
    
    Adding submodule update tests

commit 574c5049374628a1d167e0d3454e9fac6972c328
Merge: d6dd2f8 85892a9
Date:   Fri Sep 22 09:07:25 2017 -0400

    Merge pull request #2565 from RosettaCommons/aleaverfay/rs_parser_scripvars_fix
    
    parse_rosetta_script application now uses the script_vars option
    
    Fixing script-vars issue in parse_rosetta_script and validate_rosetta_script where the RosettaScriptsParser was ignoring the command line options

commit d6dd2f80ab9a57feb08fcc651a7f995dde820c4c
Merge: e8575a8 37df134
Date:   Thu Sep 21 15:13:29 2017 -0700

    Merge pull request #2548 from RosettaCommons/basantab/fix_rotamers_HBNet
    
    Fixing bug in HBNet option use_only_input_rot_for_start_res

commit e8575a8572dd02db1f782231d8f0d082b19ad195
Merge: 792bc27 3c4a90a
Date:   Thu Sep 21 13:15:35 2017 -0600

    Merge pull request #2570 from RosettaCommons/sergey/f
    
    Updating 'scripts.pyrosetta' test so it add stdout and stderr into subtest logs.

commit 792bc27409046bf9fa0e43dc352851cb00e359fa
Merge: cfe7327 c078820
Date:   Thu Sep 21 12:14:32 2017 -0700

    Merge pull request #2547 from RosettaCommons/bfrenz/cart_bonded_ring_fix
    
    Bfrenz/cart bonded ring fix

commit cfe7327c89784a8cde099cb07f94ad0a6c6e5cac
Merge: 239b493 d424927
Date:   Wed Sep 20 16:52:47 2017 -0400

    Merge pull request #2567 from RosettaCommons/guffysl/lmcs_bugfix
    
    Guffysl/lmcs bugfix

commit 239b493e96f8f5e40ddfdd62f58f9b3002411f65
Merge: a19ad2e 100dd3f
Date:   Wed Sep 20 14:24:44 2017 -0600

    Merge pull request #2561 from RosettaCommons/sergey/f
    
    Disabling incremental Binder/LLVM rebuild. Updating pyrosetta_scripts submodule.

commit a19ad2ea80d9e9e4c5e99a617b8c2941a5b5e5ba
Merge: 82c1fe4 e5355fa
Date:   Tue Sep 19 09:49:00 2017 -0700

    Merge pull request #2562 from RosettaCommons/xingjiepan/move_SSShapeComplementarityFilter_to_protocols
    
    Migrate SSShapeComplementarityFilter from devel to protocols

commit 82c1fe4853fb989ef72f7e145546e394323d763b
Merge: 839226a d2aeeb6
Date:   Mon Sep 18 15:54:56 2017 -0500

    Merge pull request #2550 from RosettaCommons/roccomoretti/fix_release_unit_tests
    
    Fix unit tests in release mode
    
    We had some unit tests which were failing when run in release mode. This PR should fix them.
    
    This PR also adds a new scons compilation mode, release_symbols, which is release mode with debugging symbols enabled. (This differs from release_debug, which is debug mode with release-mode optimizations turned on. The main difference is whether debug_asserts are active or not.)

commit 839226a33c427862a8be7b4ca555493368c1485c
Merge: 46dcc1b 648d663
Date:   Mon Sep 18 10:39:53 2017 -0700

    Merge pull request #2544 from RosettaCommons/everyday847/riboswitches
    
    Superimpose alignment error caught while doing riboswitch development

commit 46dcc1b1c7a82df5d5c8f7b3b306c7ea053fa4c9
Merge: 4c42bfa acddd1b
Date:   Sat Sep 16 13:21:44 2017 -0700

    Merge pull request #2559 from RosettaCommons/vmullig/threadsafe_elec2
    
    Fix a thread safety issue in FA_ElecEnergy method: scratch space was shared between cloned instances
    
    The scratch space object was being deep-cloned by the `FA_ElecEnergy::clone()` operation.  Now, the operation creates new scratch space.  I _think_ this will solve the problem that I'm seeing on Blue Gene by ensuring that the scratch space object is always thread-local.
    
    Tasks:
    - [x] Fix the cloning issue.
    - [x] Beauty.
    - [x] Test on Blue Gene/Q.
    - [x] Check unit tests.
    - [x] Check integration tests.
    - [x] Beautify (since master is not beautiful).

commit 4c42bfab1ced584fbdcbe081d6cfaeb304911004
Date:   Sat Sep 16 05:04:58 2017 -0400

    RosettaAI: Setting rosetta_scripts_scripts submodule to latest origin/master version.

commit 8c81945a41ea41734ed791a9001082050d3167d7
Date:   Fri Sep 15 20:06:08 2017 -0400

    RosettaAI: Setting pyrosetta_scripts submodule to latest origin/master version.

commit 42082d31e20ac4005308ba2edc9f0afa9746840d
Date:   Fri Sep 15 20:00:22 2017 -0400

    RosettaAI: Setting pyrosetta_scripts submodule to latest origin/master version.

commit eca6c6b09570652608cdde96b5edbef50bf406fe
Merge: 16e25a4 9903b0a
Date:   Fri Sep 15 12:38:35 2017 -0600

    Merge pull request #2549 from RosettaCommons/sergey/binder
    
    PyRosetta update:
    - Fixing StructFileRep::chains issue
    - Adding minimal bindings for std::set's classes

commit 16e25a4ef5c64dda773da1f4df0844cf19dd852f
Merge: a5895a8 7d5d220
Date:   Thu Sep 14 23:34:07 2017 -0400

    Merge pull request #2307 from RosettaCommons/arubenstein/enzscore_defaults
    
    Added defaults to EnzScore filter to fix bug regarding the setting of data variables resnum and whole_pose

commit a5895a8ebe9e35a7fedcc764526e81785c86ed42
Merge: 664dc0e 3dac368
Date:   Thu Sep 14 13:00:29 2017 -0700

    Merge branch 'egurapha/remodel_2ct_fix'
    Fixed incorrect terminus handling in Remodel -two_chain_tree

commit 664dc0e87ed6093b904a5139fe52520c3c6eae90
Date:   Thu Sep 14 14:53:35 2017 -0400

    Updating Binder submodule

commit 4a867320e60d61a95bbd2cc0ad08bab418cad5c1
Merge: 1037928 7e4f552
Date:   Thu Sep 14 09:54:55 2017 -0700

    Merge pull request #2546 from RosettaCommons/everyday847/better_align_pdb
    
    A better align_pdb

commit 10379286ec3c3d9832d146c3efad4f1ad6c248c9
Merge: be2c725 7455fe4
Date:   Wed Sep 13 15:23:03 2017 -0500

    Merge pull request #2545 from RosettaCommons/roccomoretti/utf_decode_replace
    
    Be more robust with UTF parsing.
    
    Add errors=replace to the UTF decode statements in Python scripts. Instead of crashing when input contains non-parsable data, replace it with the codepoint-missing character.
    
    Doesn't completely solve the issue, as Python2 will still crash when redirecting Unicode-containing characters. -- That's not really something we can fix from within the script, though. You need to set the `PYTHONIOENCODING` environment variable in the launching shell to `utf_8` or equivalent.

commit be2c7251d71c996075b86317d1466cff57074469
Merge: 902229d f2b0c20
Date:   Tue Sep 12 11:15:56 2017 -0500

    Merge pull request #2537 from RosettaCommons/roccomoretti/fix_missing_with_make_from_annotated
    
    Fix bug with nullptr in make_pose_from_sequence.
    
    ResidueTypeSet::name_mapOP can return a nullptr. This is an issue within make_pose_from_sequence(), if the sequence requires a residue that is unknown. With current master, this results in a segfault. This PR should fix that.

commit 902229d852007465c5e2aabc701a5d0e8a9b5f1b
Merge: ae96acd 4f5e040
Date:   Tue Sep 12 11:15:13 2017 -0500

    Merge pull request #2536 from RosettaCommons/roccomoretti/vector_normalize_issue
    
    Metal constraint fixes & better diagnostics.
    
    * In a recent master, there's an issue with the Enzdes/metal constraint code when the constraints add additional virtual tracking atoms. Fix this such that when we replace_residue_keeping_all_atom_positions() we don't crash if the new residue has more virtual atoms than the starting residue.
    
    * Normalizing a zero-length vector isn't necessarily bad user input, so we shouldn't throw an exception which will result in all nstruct for this input to be canceled. Also provide better diagnostic info in certain conditions.

commit ae96acdba8d9c67b2c564018ef0416443be8d335
Merge: 68aecbb b2f1bf9
Date:   Mon Sep 11 13:54:29 2017 -0600

    Merge pull request #2508 from RosettaCommons/benchmark
    
    Adding automatic testing for scripts in pyrosetta_scripts repository
    
    - Adding 'scripts' benchmark-script for testing Rosetta/PyRosetta scripts submodules
    - Adding https://github.com/RosettaCommons/pyrosetta_scripts submodule mounted at main/pyrosetta_scripts
    - Updating pyrosetta_scripts with demo app and tests (see RosettaCommons/pyrosetta_scripts#3)
    -  Adding scripts.rosetta.* testing scripts (see RosettaCommons/rosetta_scripts_scripts#1)

commit 68aecbb751cf5ecac2857b4e186937abe9907732
Merge: c00609f 1182750
Date:   Mon Sep 11 11:56:49 2017 -0500

    Merge pull request #2541 from RosettaCommons/roccomoretti/ligand_rmsd_native_ensemble_best
    
    Add ability to get an 'ensemble best' from the ligand docking RMSD.
    
    If you enable the 'native_ensemble_best' option in the InterfaceScoreCalculator, you can provide a native with multiple residues in the given chain. The native comparisons (e.g. ligand_rmsd) will then be reported for the best (i.e. lowest rmsd) structure.

commit c00609f9482dbbc3116f0af36cfd788f49fa243d
Merge: 31ad7bd 8696637
Date:   Sat Sep 9 12:18:47 2017 -0600

    Merge pull request #2540 from RosettaCommons/sergey/binder
    
    Adding explicit instantiation of vector0< core::io::AtomInformation >

commit 31ad7bd3103066b7395e08bc61ae576f35c86544
Merge: e707098 27cb72a
Date:   Fri Sep 8 14:05:39 2017 -0400

    Merge pull request #2530 from RosettaCommons/Cyrus/mergetarget
    
    Cyrus/mergetarget
    
    Two code packets from Steven Lewis from Cyrus:
    
    a) IndependentLoopMover internally tracks the status of the loops it is trying to close, but does not REPORT that status (or perhaps it reports it to a checkpointing file, which is useless to non-BOINC clients). Changes to that class are to expose that loop status so calling code can check closure status.
    
    b) SingleLigandRotamerLibrary previously accepted rotamers only via the PDB_ROTAMERS line in a params file, or rotamers generated within Rosetta. I have rearranged this functionality so that a PDB-formatted set of rotamers (the same data that might come in from disk via PDB_ROTAMERS) can come in from a more generic input stream object. In other words SingleLigandRotamerLibrary no longer requisitely reads from disk to initialize itself. This class, and also StoredRotamerLibrarySpecification, gain unit tests.

commit e70709889d28c907c9edef7a3ecc7969374b615a
Merge: cbd8d53 17cb490
Date:   Fri Sep 8 09:06:48 2017 -0400

    Merge pull request #2534 from RosettaCommons/aleaverfay/rename_just_parse_a_script
    
    Aleaverfay/rename just parse a script
    
    As part of the get-out-the-scripts drive, I'm adding two public apps:
    
    * validate_rosetta_script, and
    * parse_rosetta_script
    
    based on Andy Watkins' prior just_parse_a_script pilot app. The purpose of these two applications is to validate an XML file against Rosetta's internally-generated XSD (validate_rosetta_script) and to create all of the Movers/Filters/TaskOperations/etc. in the XML file ensuring that their parse-my-tag functions all run smoothly (parse_rosetta_script). In both cases, if the input XML file is ok, then the applications print out a short success message and exit with a zero exit status. If either fail, then they print out the message of any exception that was thrown and then exit with a non-zero (1) exit status.
    
    I have written application-level documentation for them in the documentation/ repository.

commit cbd8d5308224f77c56fe9850cd523cec24810f42
Merge: 9edd1b8 b5435f0
Date:   Thu Sep 7 14:13:17 2017 -0700

    Merge pull request #2524 from RosettaCommons/everyday847/two_bugs
    
    Condition one of Vikram's new features -- for now -- on non-RNA identity

commit 9edd1b807df39403eee0887e4120470f8c9e98d5
Merge: 9fe68d1 c470bc2
Date:   Thu Sep 7 13:45:55 2017 -0700

    Merge pull request #2502 from RosettaCommons/everyday847/builders
    
    Add 'builders' for common RNA protocols

commit 9fe68d13ede2dba3a5fa0caad9a7a95bd6dde16b
Merge: 088978b f102c36
Date:   Thu Sep 7 12:00:01 2017 -0500

    Merge pull request #2532 from RosettaCommons/jadolfbr/unused_sugar_options
    
    Remove antiquated option that simply gives a warning now for sugars.
    
    (Integration tests are cosmetic as expected)

commit 088978bc5c7722ef423819955ac280f0f4d86402
Merge: 627468c c8a8fb9
Date:   Thu Sep 7 11:58:14 2017 -0500

    Merge pull request #2526 from RosettaCommons/jadolfbr/carb_params_talaris
    
    Talaris Glycan Params
    
    Updates the Talaris glycan params with those from REF2015 to prepare for benchmarking.

commit 627468cc8b930cd973d5c5a350de0efeb3db6734
Merge: 5cce9fa e888bb2
Date:   Thu Sep 7 09:15:19 2017 -0400

    Merge pull request #2413 from RosettaCommons/aleaverfay/jd3_multithreaded_jd_take3
    
    I've extracted the rather complex logic of asking the JobQueen for the next job to run out of the MPIWorkPoolJobDistributor and into a new class, the JobExtractor. I've replaced the original logic from the MPIWorkPoolJobDistributor with the JobExtractor class, and that looks like it works just fine.
    
    So writing the (single-process) MultiThreadedJobDistributor then becomes very easy: pop a job from the Extractor, put it into a work-queue, let a thread pool get to it when the next thread becomes available.
    
    This implementation makes use of the Apache2-licensed C++ Thread Pool Library (CTPL); it works incredibly smoothly.

commit 5cce9fa5d36219529518ed4cdf1058d41eda6cb5
Merge: 522ad27 238b1d51
Date:   Wed Sep 6 14:04:29 2017 -0500

    Merge pull request #2531 from RosettaCommons/jadolfbr/update_vax_settings
    
    Updating SchiefLab cluster site.settings

commit 522ad273e4bf3dbceef15b24b8780440892b67b6
Merge: 344297e e822a2e
Date:   Wed Sep 6 10:21:45 2017 -0400

    Merge pull request #2518 from RosettaCommons/jadolfbr/code_template_dir
    
    Add robustness to Code Template outdir option.
    
    More robustly fail with not using correct dir options full paths or not-quite-relative paths.  Add ability to use slashes with options just in case by splitting them.  We won't fail, but we also prefer lists due to complete relative paths.  Should help new users as found in BootCamp.

commit 344297e6a09fb5a96d212c6965373f442df61c42
Merge: d6547f6 88e4f81
Date:   Tue Sep 5 23:28:50 2017 -0700

    Merge pull request #2529 from RosettaCommons/vmullig/correct_nomenclature
    
    Correct my nomenclature in certain movers, filters, and protocols that work with mirror symmetry.
    
    I incorrectly had "cN/m" instead of "sN".